Analyzing Multi-Omics Data in Adult Soft Tissue Sarcomas

The cBioPortal for Cancer Genomics repository was utilized to reanalyze multi-omics data from the Cancer Genome Atlas [Adult Soft Tissue Sarcomas (TCGA, Cell 2017)]^{29 (link),30}. Genomic and transcriptomic data from 206 patients representing three different sarcoma types (Soft tissue Sarcoma, Uterine Sarcoma and Nerve Sheath Tumor) with seven different cancer subtypes [Leiomyosarcoma (25.7%), Dedifferentiated Liposarcoma (24.3%), Undifferentiated Pleomorphic Sarcoma (21.4%), Uterine Leiomyosarcoma (13.1%), Myxofibrosarcoma (8.3%), Synovial Sarcoma (4.9%), Malignant Peripheral Nerve Sheath Tumor (2.4%)] were analyzed. A list of CNTNAP4 interacting genes (CNTNAP3B, APBA1, CNTNAP2, NELL1, CASK, TIAM1, AFDN, NRXN3, MACF1, NRXN2, CCDC184, FBXO21, MAST3, RANBP10) was analyzed. The OncoPrint provided the genetic alteration frequency on the DNA level for the different cancer types for the queried gene list. Genetic alterations were further divided into missense mutations, amplification, deep deletion, and multiple alterations. From the same platform, we obtained the overall patient survival status.

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Qin Q., Ramesh S., Gomez-Salazar M., Zhong L., Cherief M., Pratapneni A., Morris C.D., McCarthy E.F., Zhang X, & James A.W. (2023). CNTNAP4 signaling regulates osteosarcoma disease progression. NPJ Precision Oncology, 7, 2.

Publication 2023

A genes Adult Afdn Cancer Cancer gene Cell Cntnap2 Dedifferentiated liposarcoma Deletion Genetic alterations Genomic Leiomyosarcoma Malignant peripheral nerve sheath tumor Missense mutations Nerve sheath tumor Patient Sarcoma Synovial sarcoma Tiam1 Transcriptomic Undifferentiated pleomorphic sarcoma Uterine

Corresponding Organization :

Other organizations : Johns Hopkins University, University of California, Los Angeles

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Variable analysis

independent variables

Genetic alterations (missense mutations, amplification, deep deletion, and multiple alterations) in the list of CNTNAP4 interacting genes (CNTNAP3B, APBA1, CNTNAP2, NELL1, CASK, TIAM1, AFDN, NRXN3, MACF1, NRXN2, CCDC184, FBXO21, MAST3, RANBP10)

dependent variables

Genetic alteration frequency on the DNA level for the different cancer types
Overall patient survival status

control variables

Control variables not explicitly mentioned

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